FastaLake selects compact metaproteomic databases from large sequence reservoirs by de novo peptide lookup
- 1Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
Abstract
Metaproteomics analyses require protein sequence databases, yet the microbial proteins present in complex communities are not known in advance. Searching reference catalogs containing hundreds of millions of candidate sequences reduces identification sensitivity, while generating sample-specific databases through metagenomic sequencing adds time and cost. We introduce FastaLake, a computational workflow that uses full-length de novo peptide predictions by AlphaNovo to retrieve complete proteins from broad sequence resources and selects compact databases for conventional searching. In a defined eight-member community, FastaLake approached reference-search peptide yields without knowing its members. Using public sequence catalogs, FastaLake identified about as many peptides as matched metagenomic databases in two stool cohorts and 20-35% more in intestinal fluid at the same nominal 1% peptide false discovery rate. The resulting proteomes reveal personal functional profiles that persist across intestinal regions despite differences in leading species between intestinal fluid and stool. DNA, RNA and protein profiles agreed on broad differences between patients but only weakly on individual functions. All 726 acquisition-specific databases were smaller than the human reference proteome. Compact databases allowed non-specific searches of all 347 CapScan acquisitions, revealing histidine enrichment at peptide C termini in intestinal fluid. FastaLake enables metaproteomics analysis without matched metagenomic sequencing by constructing search databases from sequence resources and de novo peptide sequencing.
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BibTeX
@misc{treit2026fastalake,
title = {{FastaLake selects compact metaproteomic databases from large sequence reservoirs by de novo peptide lookup}},
author = {P. V. Treit and F. A. Rosenberger and P. Hartout and M. Lebedev and J. Xiao and M. Zwiebel and P. E. Geyer and A. Sinha and G. Wallmann and V. Brennsteiner and K. Korff and E. H. Rodriguez and W.-F. Zeng and M. T. Strauss and M. I. Keller and M. Kuhn and J. Trebicka and C. Junot and M. Arumugam and J. A. Grembi and D. Shalon and K. C. Huang and K. Borgwardt and J. B. Mueller-Reif and M. Mann},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.08.757395},
url = {https://www.biorxiv.org/content/10.64898/2026.10.08.757395v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - FastaLake selects compact metaproteomic databases from large sequence reservoirs by de novo peptide lookup
AU - P. V. Treit
AU - F. A. Rosenberger
AU - P. Hartout
AU - M. Lebedev
AU - J. Xiao
AU - M. Zwiebel
AU - P. E. Geyer
AU - A. Sinha
AU - G. Wallmann
AU - V. Brennsteiner
AU - K. Korff
AU - E. H. Rodriguez
AU - W.-F. Zeng
AU - M. T. Strauss
AU - M. I. Keller
AU - M. Kuhn
AU - J. Trebicka
AU - C. Junot
AU - M. Arumugam
AU - J. A. Grembi
AU - D. Shalon
AU - K. C. Huang
AU - K. Borgwardt
AU - J. B. Mueller-Reif
AU - M. Mann
PY - 2026
DA - 2026/10/08
PB - bioRxiv
DO - 10.64898/2026.10.08.757395
UR - https://www.biorxiv.org/content/10.64898/2026.10.08.757395v1
AB - Metaproteomics analyses require protein sequence databases, yet the microbial proteins present in complex communities are not known in advance. Searching reference catalogs containing hundreds of millions of candidate sequences reduces identification sensitivity, while generating sample-specific databases through metagenomic sequencing adds time and cost. We introduce FastaLake, a computational workflow that uses full-length de novo peptide predictions by AlphaNovo to retrieve complete proteins from broad sequence resources and selects compact databases for conventional searching. In a defined eight-member community, FastaLake approached reference-search peptide yields without knowing its members. Using public sequence catalogs, FastaLake identified about as many peptides as matched metagenomic databases in two stool cohorts and 20-35% more in intestinal fluid at the same nominal 1% peptide false discovery rate. The resulting proteomes reveal personal functional profiles that persist across intestinal regions despite differences in leading species between intestinal fluid and stool. DNA, RNA and protein profiles agreed on broad differences between patients but only weakly on individual functions. All 726 acquisition-specific databases were smaller than the human reference proteome. Compact databases allowed non-specific searches of all 347 CapScan acquisitions, revealing histidine enrichment at peptide C termini in intestinal fluid. FastaLake enables metaproteomics analysis without matched metagenomic sequencing by constructing search databases from sequence resources and de novo peptide sequencing.
ER -